SeqScape Software Version 2.1 User Guide - InfoNet

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Sample Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15 Displaying the Sample Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15 Viewing Variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-20 Saving Your Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-21 About the Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22 Types of Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22 Exporting and Printing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22 Viewing the Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-23 Viewing the Reports and Project Results . . . . . . . . . . . . . . . . . . . . . . 7-25 Analysis QC Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26 Mutations Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28 AA Variants Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-31 Specimen Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32 Sequence Confirmation Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-33 Base Frequency Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-34 Library Search Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-35 RDG Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-37 Audit Trail Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-38 Genotyping Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-39 Customizing the Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-42 Customizing Text Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-42 Customizing the Data View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-44 Chapter 8 Reanalyzing and Editing Data Workflow for This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2 About Analysis Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3 Viewing Analysis Parameters in the Sample Manager . . . . . . . . . 8-4 Changing the Analysis Parameters in the Sample Manager . . . . . . . . 8-6 Adding Samples to the Sample Manager . . . . . . . . . . . . . . . . . . . 8-6 Changing Basecaller and DyeSet/Primer Files . . . . . . . . . . . . . . . 8-6 Changing the Analysis Parameters in an Analysis Protocol . . . . . . . . . 8-7 Editing an Analysis Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-7 Applying the Analysis Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . 8-12 viii ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 3:10 pm, SeqScapeUGTOC.fm
Editing the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-13 About Sequence Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-13 When to Edit the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-13 Editing a Sample or a Consensus Sequence . . . . . . . . . . . . . . . . . . . 8-14 Editing a Consensus Sequence in the Segment View . . . . . . . . . 8-14 Editing Sample Bases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-14 Editing a Consensus Sequence in the Project View . . . . . . . . . . . 8-15 Adjusting the Clear Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-16 About the Clear Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-16 Using the Clear Range Widget . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-17 Using the Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-18 Using the Set Clear Range Dialog Box . . . . . . . . . . . . . . . . . . . . . 8-19 Editing Variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-20 Method 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-20 Method 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-21 Saving Your Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-21 Adding a Genotype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-22 Chapter 9 Exporting and Printing Data and Reports Exporting Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3 File Names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3 Format Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3 Exporting a Project Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4 Exporting a Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5 Exporting a Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6 Exporting a Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-7 Exporting Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-8 File Names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-8 Format Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-8 Exporting a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-9 Exporting All Reports Automatically . . . . . . . . . . . . . . . . . . . . . . . 9-10 Printing Data and Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-11 Customizing Header and Footer Display . . . . . . . . . . . . . . . . . . . 9-11 Printing Views of a Sample File . . . . . . . . . . . . . . . . . . . . . . . . . . 9-12 Printing Various Views of a Project . . . . . . . . . . . . . . . . . . . . . . . . 9-14 Printing a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-16 ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 3:10 pm, SeqScapeUGTOC.fm ix
Page 1 and 2: ABI PRISM ® SeqScape ® Software V
Page 3 and 4: Contents Preface How to Use This Gu
Page 5 and 6: Specifying the Analysis Settings .
Page 7: Adding Specimens and Importing Data
Page 11 and 12: Understanding the Autoanalysis Mana
Page 13 and 14: Appendix G Software Warranty Comput
Page 15 and 16: Preface How to Use This Guide Purpo
Page 17 and 18: Conventions Used in This Guide Safe
Page 19 and 20: How to Obtain Services and Support
Page 21 and 22: Introduction to ABI PRISM SeqScape
Page 23 and 24: For Users of Earlier Versions of Se
Page 25 and 26: About SeqScape Software About SeqSc
Page 27 and 28: About SeqScape Software How the Sof
Page 29 and 30: Getting Started 2 2 This chapter co
Page 31 and 32: Hardware and Software Requirements
Page 33 and 34: SeqScape Software Versions SeqScape
Page 35 and 36: Installing the Full Version for the
Page 37 and 38: Removing SeqScape Software Removing
Page 39 and 40: Starting SeqScape Software for the
Page 49 and 50: New Users Logging In for the First
Page 51 and 52: SeqScape Software Structure Project
Page 53 and 54: SeqScape Software Toolbar The secon
Page 55 and 56: Menus on the Main SeqScape Window C
Page 57 and 58: Creating Analysis Defaults and Disp
Page 59 and 60:
Analysis Defaults Settings Analysis
Page 61 and 62:
Creating Analysis Protocols 5. Sele
Page 63 and 64:
Creating Analysis Protocols Specify
Page 65 and 66:
Creating Analysis Protocols 2. Sele
Page 67 and 68:
Creating Analysis Protocols 2. Ente
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Specifying the Analysis Settings If
Page 71 and 72:
Specifying the Analysis Settings 4.
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Specifying the Analysis Settings 6.
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Specifying Display Settings To spec
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Specifying Display Settings 5. Sele
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Specifying Display Settings d. To d
Page 81 and 82:
Creating a Reference Data Group 4 4
Page 83 and 84:
Reference Data Group (RDG) Referenc
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Reference Data Group (RDG) Download
Page 87 and 88:
Creating a New RDG Using the Wizard
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Page 91 and 92:
Page 93 and 94:
Creating a New RDG Using SeqScape M
Page 95 and 96:
Defining Regions of Interest (ROI)
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Defining Regions of Interest (ROI)
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ROI Tab Descriptions Columns in the
Page 101 and 102:
Creating a Library Setting Up Your
Page 103 and 104:
Creating a Library 8. Select a laye
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Creating New Layers The Library Edi
Page 107 and 108:
Creating New Layers Adding a Refere
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Declaring Variants into an RDG Decl
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Declaring Variants into an RDG 4. I
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Declaring Variants into an RDG 6. A
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Creating an RDG from Aligned Consen
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Creating a Project Template 5 5 Thi
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Creating a Project Template Creatin
Page 127 and 128:
Saving Project Components Saving Pr
Page 129 and 130:
Creating and Analyzing a Project 6
Page 131 and 132:
Workflow for This Chapter Before Yo
Page 133 and 134:
Using the New Project Wizard to Cre
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Page 137 and 138:
Page 139 and 140:
Adding Specimens and Importing Data
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Analyzing the Data 5. Click OK. A n
Page 151 and 152:
Reanalyzing a Project Using a Diffe
Page 153 and 154:
Incorporating Variants into the Pro
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Viewing the Results 7 7 This chapte
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About the Project Data About the Pr
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Project Views Table 7-1 Project Vie
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Page 173 and 174:
Segment Views Segment Views There a
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Segment Views Table 7-2 Segment Vie
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Sample Views Sample Views The sampl
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Sample Views Table 7-4 Sample Views
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Sample Views Table 7-4 Sample Views
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Viewing Variants Method 2 1. Open t
Page 185 and 186:
Viewing the Reports Viewing the Rep
Page 187 and 188:
Viewing the Reports and Project Res
Page 189 and 190:
Analysis QC Report Figure 7-3 Analy
Page 191 and 192:
Mutations Report The Mutations repo
Page 193 and 194:
AA Variants Report AA Variants Repo
Page 195 and 196:
Sequence Confirmation Report Sequen
Page 197 and 198:
Library Search Report Library Searc
Page 199 and 200:
RDG Report RDG Report The report co
Page 201 and 202:
Genotyping Report Genotyping Report
Page 203 and 204:
Genotyping Report Figure 7-12 Genot
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Customizing the Reports 2. Select o
Page 207 and 208:
Reanalyzing and Editing Data 8 8 Th
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About Analysis Parameters About Ana
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About Analysis Parameters Table 8-1
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Changing the Analysis Parameters in
Page 215 and 216:
Page 217 and 218:
Page 219 and 220:
Editing the Data Editing the Data A
Page 221 and 222:
Editing a Sample or a Consensus Seq
Page 223 and 224:
Adjusting the Clear Range The three
Page 225 and 226:
Adjusting the Clear Range Using the
Page 227 and 228:
Editing Variants Method 2 To view a
Page 229 and 230:
Exporting and Printing Data and Rep
Page 231 and 232:
Exporting Data Files Exporting Data
Page 233 and 234:
Exporting Data Files Exporting a Sp
Page 235 and 236:
Exporting Data Files Exporting a Sa
Page 237 and 238:
Exporting Reports Exporting a Repor
Page 239 and 240:
Printing Data and Reports Printing
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Printing Data and Reports 3. Select
Page 243 and 244:
Printing Data and Reports 4. Select
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Printing Data and Reports 6. Use th
Page 247 and 248:
Printing Data and Reports Table 9-3
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Sample and Consensus Quality Values
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Sample Quality Values Sample Qualit
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Consensus Quality Values Consensus
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Displaying Quality Values Customizi
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Displaying Quality Values Displayin
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Cumulative Quality Value Scoring in
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Cumulative Quality Value Scoring in
Page 263 and 264:
Automating Analysis 11 11 This chap
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Integrating SeqScape and Data Colle
Page 267 and 268:
Before You Start Is SeqScape proper
Page 269 and 270:
Launching Autoanalysis Manger Launc
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Creating Required Files in the Data
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Page 283 and 284:
Page 285 and 286:
Scheduling and Starting a Run 2. Cl
Page 287 and 288:
Understanding the Autoanalysis Mana
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Understanding the Autoanalysis Mana
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Basecallers and DyeSet/Primer Files
Page 293 and 294:
Definitions and Naming The DyeSet/P
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ABI PRISM SeqScape Software v2.1 Us
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Page 305 and 306:
Page 307 and 308:
Page 309 and 310:
Frequently Asked Questions B B This
Page 311 and 312:
Training and Documentation FAQs Tra
Page 313 and 314:
General SeqScape Software FAQs Gene
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General SeqScape Software FAQs Tabl
Page 317 and 318:
SeqScape Manager FAQs SeqScape Mana
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SeqScape Manager FAQs Table B-5 Seq
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SeqScape Manager FAQs Table B-5 Seq
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Mutation, Variant, HIM, and HFM Det
Page 325 and 326:
Data Analysis FAQs Table B-8 Data A
Page 327 and 328:
Quality Values FAQs Table B-9 Analy
Page 329 and 330:
Audit Trail, Security, and Access C
Page 331 and 332:
Translation Tables C C This appendi
Page 333 and 334:
IUPAC Diagrams IUPAC Diagrams IUPAC
Page 335 and 336:
Amino Acid Abbreviations Amino Acid
Page 337 and 338:
User Privileges D D Tables of User
Page 339 and 340:
Tables of User Privileges Table D-2
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Page 343 and 344:
Page 345 and 346:
Page 347 and 348:
Aligned Variant and FASTA File Form
Page 349 and 350:
FASTA File Format FASTA File Format
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FASTA File Format Table E-1 Accepte
Page 353 and 354:
Creating a Multi-Aligned FASTA File
Page 355 and 356:
Method 1: Create a Multi-Aligned FA
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Page 359 and 360:
Page 361 and 362:
Software Warranty G G Computer Conf
Page 363 and 364:
Limited Product Warranty Warranty L
Page 365 and 366:
Glossary ABI basecaller administrat
Page 367 and 368:
DyeSet/Primer file export FASTA for
Page 369 and 370:
Sample Manager sample quality value
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Index Numerics 310 Basecaller and D
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creating a library 4-20 an RDG, abo
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learning software, wizard 4-6 libra
Page 377 and 378:
S sample bases, editing 8-14 data,
Page 380:
Headquarters 850 Lincoln Centre Dri
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